During the preproduction phase of Gardens of Stone, Gian-Carlo was given the responsibility of filming the rehearsals. He was also responsible for supervising the electronic cinema staff. There was also potential for Gian-Carlo to intern with director, Steven Spielberg, to work on television series, Amazing Stories before his passing. Director, Penny Marshall, had also hired Gio to work on the second unit for her feature film, Jumpin' Jack Flash.

Coppola was killed in a speedboating accident on Memorial Day, 1986 at the age of 22 in Annapolis, Maryland. Griffin O'Neal, who was piloting the boat, had attempted to pass between two slow-moving boats, unaware that both boats were connected by a towline. While O'Neal barely had time to duck, Coppola was struck and killed.[1] At the time of the incident, O'Neal was being directed by Francis Ford Coppola in Gardens of Stone and was subsequently replaced. O'Neal was later charged with manslaughter over the accident. He ultimately pleaded guilty to the lesser charge of "negligent operation of a boat", was fined $200 and sentenced to 18 months probation in 1987. He eventually received an 18-day jail sentence for not performing 400 hours of community service as ordered.

At the time of his death, Coppola's fiancee, Jacqui de la Fontaine, was two months pregnant with their only daughter, Gian-Carla "Gia" Coppola (born on January 1, 1987). Gia is a writer-director, having made the 2013 film Palo Alto.

Francis Ford Coppola subsequently dedicated 1988's Tucker: The Man and His Dream to Gio's memory due to his love of cars and for unwittingly inspiring the elder Coppola to revive the production of the long-gestating film and finishing it. A scene in Francis Ford Coppola's 2011 film Twixt shows the death of a character as having happened in the same manner as Gio's death.

At the Inglenook winery, owned by Eleanor and Francis in Napa, California, there is a 12-acre vineyard named the 'Gio vineyard,' after Gian-Carlo by the workers, which was planted in 1988.

Eleanor Coppola's touring art installation, 'Circle of Memory,' commemorates the life of Gian-Carlo and has been exhibited in San Diego, Oakland, Sante Fe, Montpellier, Salzburg, Stockholm and Oslo.